Variant report

Variant	rs12902622
Chromosome Location	chr15:59855226-59855227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59843949..59845502-chr15:59854389..59856261,2	MCF-7	breast:
2	chr15:59824741..59825604-chr15:59854999..59855608,3	MCF-7	breast:
3	chr15:59854619..59857968-chr15:59858915..59861459,3	MCF-7	breast:
4	chr15:59824873..59825654-chr15:59854728..59855447,3	K562	blood:

Variant related genes	Relation type
ENSG00000240238	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10083653	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10152904	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10163153	1.00[CEU][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs11853187	0.96[ASN][1000 genomes]
rs11856306	0.96[ASN][1000 genomes]
rs11856554	0.84[EUR][1000 genomes]
rs11856580	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12438840	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440292	0.88[CEU][hapmap];0.93[MEX][hapmap];0.81[EUR][1000 genomes]
rs12908589	0.86[EUR][1000 genomes]
rs12914046	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1552033	0.88[CEU][hapmap]
rs1552034	0.87[CEU][hapmap]
rs17236671	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17269684	1.00[CEU][hapmap];0.92[MEX][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28514722	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34444281	0.83[EUR][1000 genomes]
rs34642067	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35384735	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35461856	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35743616	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36034625	0.86[EUR][1000 genomes]
rs4419005	0.86[EUR][1000 genomes]
rs4597252	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71480534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71480535	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71480536	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7179805	0.84[EUR][1000 genomes]
rs7342617	0.88[ASN][1000 genomes]
rs8036403	0.88[CEU][hapmap]
rs8037054	0.88[CEU][hapmap]
rs8041216	0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv527754	chr15:59848471-59855226	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59841600-59861600	Weak transcription	Gastric	stomach
2	chr15:59848800-59857600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:59851000-59859000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:59853600-59855600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr15:59853800-59861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:59855000-59858800	Weak transcription	Hela-S3	cervix

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